Marker Genes • nicheDE

Finding Marker Genes in an Index Cell Type Between Two Niche Cell Types

Given two niche cell types, $n_1$ and $n_2$ , and an index cell type $i$ the purpose of niche marker gene analysis is to find genes in which the effect of $n_1$ on $i$ ’s gene expression is greater than the effect of $n_2$ on $i$ ’s gene expression. This is done doing a contrast test of the corresponding niche-DE regression coefficents. Marker gene analysis can be done via the function ‘niche_DE_markers’ which takes in 5 arguments

Arguments

object: A niche-DE object
index: The index cell type
niche1: Niche cell type $n_1$
niche2: Niche cell type $n_2$
alpha: The FDR control level desired

Here we look for marker genes in fibroblasts near tumor cells relative to B cells. The output will be a list of marker genes with their corresponding adjusted pvalues.

#get marker genes
fibro_tum_markers = niche_DE_markers(NDE_obj,index = 'stromal',niche1='tumor_epithelial',niche2='B_plasma',0.05)
#preview output
head(fibro_tum_markers)